GEO DataSets

(Submitter supplied) To better characterize smoking–associated methylation changes in whole blood, we used Illumina HumanMethylation450 BeadChip to assess DNA samples from current (SM, n=172) and never smokers (NS, n=81).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

253 Samples

Download data: IDAT, TXT

(Submitter supplied) Tobacco smoking alters DNA methylation profiles of immune cells which may underpin some of the pathogenesis of smoking-associated diseases. However, approaches linking smoking-driven epigenetic effects in specific immune cell types with disease risk are limited. We isolated six leukocyte subtypes, CD14+ monocytes, CD15+ granulocytes, CD19+ B cells, CD4+ T cells, CD8+ T cells, and CD56+ natural killer cells, from whole blood of healthy adult smokers and nonsmokers for epigenome-wide association study (EWAS).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL29753

876 Samples

Download data: IDAT, TXT

(Submitter supplied) To investigate blood biomarkers of smokers and to provide molecular basis of B cell subtype shift from naïve to memory in smokers, total RNA from peripheral CD19+ B cells isolated from healthy adult smokers and nonsmokers was subjected to RNA-Seq and data were analyzed with covariates including age, race, sex, BMI, estimated CD4+T cell%, CD8+T cell%, natural killer (NK) cell%, monocyte%, granulocyte%, or naive B cell%.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

35 Samples

Download data: TXT

(Submitter supplied) While tobacco smoke exposure strongly influences DNA methylation and is causative in numerous human diseases, the underlying mechanistic links are obscure. Here we investigated genome-wide smoking-associated differentially methylated regions (SM-DMRs) using CD14 monocytes of smokers (n=47) and nonsmokers (n=46) from two independently recruited populations, the Multi-Ethnic Study of Atherosclerosis (MESA) and Clinical Research Unit (CRU) at NIEHS. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL18573 GPL16791

93 Samples

Download data: BEDGRAPH

(Submitter supplied) Healthy ex vivo biopsies from masticatory mucosa from 17 current and 21 never smokers were analysed using whole transcriptome RNA sequencing (16 mio reads/sample), showing significantly increased expression of CYP1B1 in smokers compared to non-smokers (p = 2.2 × 10−14), together with 13 significantly upregulated transcripts. Six transcripts were significantly downregulated.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

38 Samples

Download data: TXT

(Submitter supplied) Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: BED, BW

(Submitter supplied) Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL10558

2832 Samples

Download data

(Submitter supplied) The MESA Epigenomics and Transcriptomics Study has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes from a large study population (community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)). The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

1202 Samples

Download data: TXT

(Submitter supplied) Gene expression profiles were compared to investigate age-marking differential gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

881 Samples

Download data: TXT

(Submitter supplied) We generated genome-wide methylation levels, using whole-genome bisulfite sequencing, for sorted CD4+ cells from cordblood of newborns exposed vs. unexposed to tobacco smoke in utero

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: TXT

(Submitter supplied) Background Chronological aging-associated changes in the human DNA methylome are studied by multiple epigenome-wide association studies (EWAS); however, the aging-associated DNAmet changes identified among different age groups and tissues vary and especially the rates of aging-associated alterations in the epigenome during adulthood remain unclear. Here, we further explore and characterize CpG-sites where DNA methylation levels alter at a constant rate during adulthood and are also independent of blood cell type heterogeneity. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

184 Samples

Download data: TXT

(Submitter supplied) This study performed Illumina Methylation450 analysis of CD4+ T-cells, CD19+ B-cells and CD14+ Monocytes from lupus patients and controls. A validation cohort was further analyzed with the same platform using CD4+ T-cells, CD45RO-CD45RA+ naive T-cells, CD45RO+CD45RA- memory T-cells, and CD25+CD127- regulatory T-cells.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

434 Samples

Download data: TXT

(Submitter supplied) Background While smoking is known to associate with development of multiple diseases, the underlying mechanisms are still poorly understood. Tobacco smoking can modify the chemical integrity of DNA leading to changes in transcriptional activity, partly through an altered epigenetic state. We aimed to investigate the impact of smoking on lung cells collected from bronchoalveolar lavage (BAL). Methods We profiled changes in DNA methylation (5mC) and its oxidized form hydroxymethylation (5hmC) using conventional bisulfite (BS) treatment and oxidative bisulfite treatment with Illumina Infinium MethylationEPIC BeadChip, and examined gene expression by RNA-seq in healthy smokers. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

70 Samples

Download data: IDAT, TXT

(Submitter supplied) We aim to discover differentially methylated regions (DMRs) in peripheral T cells involved in de novo cSCC development after kidney transplantation. This was a retrospective study on biobank patient material. We matched kidney transplant patients with (future) cSCC to those without cSCC and studied genome-wide DNA methylation (450k arrays) of T cells before transplantation.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

65 Samples

Download data: IDAT

(Submitter supplied) Genome wide DNA methylation profiling of smokers and non-smokers in PBMC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across 485,577 CpGs in PBMC samples. Samples included 50 smokers and 61 non-smokers.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

111 Samples

Download data: TXT

(Submitter supplied) This study performed a genome-wide methylation analysis of positively isolated CD19+ B cells in rheumatoid arthritis (RA) and healthy controls. The Ilumina HumanMethylation450 BeadChip was uset to obtain the methylation levels at >400,000 CpG sites. Samples include 49 RA patients and 73 healthy controls.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

122 Samples

Download data: IDAT

(Submitter supplied) Genome wide DNA methylation profiling of psoriatic disease skin tissue and adjacent Normal skin samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tissue samples. Total 48 samples were taken including 24 paired tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

48 Samples

Download data: IDAT

(Submitter supplied) B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation status of 402,842 CpG-sites across the genome (Illumina 450k array) in tumor and remission samples of 46 pre-B ALL patients, thus generating the most comprehensive single CpG-site resolution pre-B ALL methylomes so far. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

92 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL10558

48 Samples

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